A statement on the FA website read: "The charge was in relation to a breach of FA Rule E3 concerning media comments which implied that the match referee and/or match officials in general are motivated by bias and/or brought the game into disrepute.
"Martinez, who had requested a personal hearing, was also warned as to his future conduct."
The Spaniard was frustrated after his side's 4-0 defeat at Old Trafford, during which England striker Danny Welbeck was awarded a controversial penalty following what seemed to be minimal contact from Ali Al Habsi.
Speaking to reporters after the match, Martinez said: "You know what he is trying to do. I have come to United three times before today and for whatever reason we don't seem to be measured in the same manner as the team at home.
"Today the penalty is as bad a decision as you are going to see in the Premier League.
"In many ways, you feel as though you are fighting against a mountain."